


Finally, a family

by Mmjohns



Category: Agents of S.H.I.E.L.D (TV), Avengers (All Media Types), Marvel, Marvel Cinematic Universe, Marvel Cinematic Universe (MCU)
Genre: Fury needs a smack, Genius Skye, Nick Fury is an asshole, Origin fix, Orphan Skye, Skye finds her family, origin fic, science!!
Language: English
Status: In-Progress
Published: 2017-09-11
Updated: 2017-09-16
Packaged: 2018-12-26 12:35:49
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 7
Words: 4,463
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/12059112
Author URL: https://archiveofourown.org/users/Mmjohns/pseuds/Mmjohns
Summary: Skye is an orphan whose only wish is for a family, and for years she has been searching for her parents. And after everything she may finally have found hers.





	1. Chapter 1

**Author's Note:**

> Errors are my own, let me know if you would like to see more, or anything in particular

Skye had spent years dreaming of this day, but now that she was actually here, she was terrified.

 

Growing up an orphan had been hard, but growing up an orphan without the tiniest clue who you were was worse. She remembers how even amongst the orphans at St. Agnes' she was pitied. Even amongst those who had so little she had less. The nuns of course gave her a name, after all they couldn't just yell "hey you" all the time. Mary Sue Poots, that was the name they gave her, she often wondered why they chose it, or if they were trying to be cruel. It made her stand out amongst the orphans even more than her mixed heritage already did, and that was certainly a curse. 

 

As she grew she endured weekly, if not daily beatings, be they from the other kids at the orphanage or from the foster families she spent so little time with. By the age of three she had already learned that truth that all orphans learn, look after yourself, no one else will. And so she became invisible wherever possible, she made sure that no one noticed her if she could avoid it, not at school, not in the homes, and most certainly not at the orphanage. 

 

This lead her to spend the majority of her time hiding in the city and by the time she learned to read at age 6 she discovered the public library. She found that she could sneak in there and no one would bother her for hours, she learnt that no one payed attention to a little kid and she learnt so much more. This was the age of computers and as she hid in the library she watched as those from the colleges came in to use the computers, they didn't care if she watched them as long as she didn't interrupt. And so she set to learning more and more, she watched as the students became more and more skilled as she herself learnt more and more and by age nine she had learnt more about computers than most adults would ever know. 

 

And so it was she turned her attention to other things, science and mathematics, and engineering, she absorbed as much as she could on these subjects. She only ever made the mistake of revealing herself once, she was in the middle of a maths class when her teacher asked her to solve a problem on the board. The speed and ease with which she solved it drew the attention of the teacher and the other students. That day she learned what it meant to be special and she had a cast for the next six weeks to remind her. After that she kept her head down and her mouth shut. 

 

By the time she was sixteen she had had enough. She was tired of being forced to hide her abilities and to pander to the beliefs of the teachers when all they saw was the poor orphan girl, and so she ran. She put her skills to use and began to hack and crack systems working her way into just about every corner of the internet. She became famous, not amongst normal people of course, but amongst those who prowl the back channels of the internet she was someone to be admired, and feared. Eventually though the novelty wore off and Skyenet as she called herself turned her abilities to more private questions.

 

She spent the next several years hacking her way through firewall after firewall using a computer she managed to win in a bet she managed to hack multimillion dollar businesses and all that had lead her to one document. 

One document redacted by SHIELD. 

 

The decision to hack SHIELD was not made lightly and so for the first time in nearly two years Skyenet went public again. As soon as she went live it was a race against time, the FBI, the CIA, the NSA, Interpol, and about 50 other agencies were on the hunt for her as soon as she reappeared. But she was smarter than them, she managed to hide herself literally everywhere, she would appear in every network all at once, and no one could find her. She began to hack SHIELD in May, and by July she was in. The truth was that finding the backdrop had been as simple as finding a cadet who didn't scan their emails properly but getting into the system took far more work. Eventually though she managed to get into the document server and find what she was searching for. The only problem was this too was redacted, however Skye was smart, brilliant some might say and she knew there had to be one person who would have access, the Director. The document was redacted by his order and so it made sense he would have the original. 

 

Surprisingly enough after that it was simple enough to get access to the Director's computer, the Pirate as she had taken to calling him wasn't as smart as he liked to believe, he used a car connected to an AI to access files while driving and that made him vulnerable. It took her three minutes to enter the DMV system and change the toll push for the bridge the Director used and then it was just a matter of waiting. Three days later she was in, she had dumped a direct access and override command into the AI that unspooled silently over the next several days and on the seventh day she had access to every file on the Director's private servers. 

 

And that was how she ended up here, New York, she had sworn that she would never return here after the hell that was her formative years but now she finds herself back here once more. And this time she can't believe her eyes. She looks up at the tower before her, no tower doesn't do it justice, monolith is far more accurate, Avenger tower, 89 stories tall and atop it all stands her father and for the first time in forever Skye actually wonders if she is ready


	2. Chapter 2

**Summary for the Chapter:**

> How to get in?

Skye stays there for nearly half an hour before she moves on, she mixes into the crowd fading away from any eyes that seek to follow before making her way to a nearby café where she had parked her van.

Finding her way to Avengers tower had been difficult but it seemed like child's play compared to actually getting inside. There was no way they were just going to let some woman off the street into the tower not with the amount of enemies they had. And there was certainly no way they would allow her to enter just because she said she was the daughter of an Avenger, there were clearly far too many women out there desperate enough to pull that stunt. 

 

And so she sat there trying to think of ways into the tower, for hours she barely moved instead watching the way that the towers defences seemed to shift and change, to open and close and reinforce themselves. Of course it was clear to her the cause of this, J.A.R.V.I.S. Tony stark's AI, he was responsible for running the tower and so far he was the only system Skye hadn't cracked. Honestly he had never been a priority before, sure he was cool, and sure he was potentially the most advanced piece of technology on the planet, but he had never been a direct problem before. She spends several hours trying to infiltrate the system, using zombie computers all over the world to probe J.A.R.V.I.S.'s defences without much luck. He was just too fast and too unpredictable for a human or script to beat, unless… the best way to beat this particular type of fire is with fire. If she wants to beat J.A.R.V.I.S she needs her own AI, a better and stronger AI.

And so she begins coding.

 

Coding an AI really isn't all that difficult, at least not compared to the quantum mechanics she had read. The best part being that as you coded parts and intertwined them together they slowly began to build on each other. Synergy, literally, greater than the sum of their parts. This was what she was building, she was birthing a living organism, it could think for itself, it could react and make decisions, but unlike so many people who got swept away in the excitement she made sure of one thing, her AI would always have a sense of morality. She may call herself Skyenet, but she has no desire to see the world end.

 

She spends weeks locked up in that van and while she doesn't agree with theft she does appropriate some money from some decidedly unfriendly criminal syndicates to buy food and other necessities. She rarely leaves being extremely careful that when she does no one could discover her project and steal the AI before it's morality has formed. Finally after three and a half months of work she is done, the AI she has built has to be the finest piece of coding she has ever done, and she can't help feeling like a proud mother the first time she brings her online.

 

She decides to name her AI Watchtower and after tapping into the encrypted military satellites she allows Watchtower to slowly spread across the globe unfolding into data centres and Supercomputers as she slowly comes to life. 

And when her computer reboots she hears a soft female voice say "Hello Skye, how may I help you today?"


	3. Hi Dad

**Summary for the Chapter:**

> Skye enters the tower and meets her father

**Notes for the Chapter:**

> I apologise for my appalling spelling, I am in Australia and we don't get decent internet at the best of times, tonight it barely works at all so I haven't been able to run my usual checks like I would in any other case. I apologise

After that it was relatively simple to get into the tower, not to brag but Watchtower was running circles around J.A.R.V.I.S. and because of this Skye was easily able to bypass the security on the rear loading dock and slip inside the building. Finding her way up proved only slightly more difficult as J.A.R.V.I.S. directly controlled all the elevators but a building this size even belonging to the Avengers needed to have stairs in case of fire. A quick check of the building plans she had hacked from The Avengers server and she found the concealed panel by the back wall quickly beginning her ascent. 

 

As she climbs she is glad for all the running she has had to do over the years, it prompted her to stay in shape and even if she has been neglecting herself in favour of building her AI she still manages to get up to the 79th floor like she intended without doubling over from exhaustion. That being said when she walks into the level and sees a giant couch she can't help the urge to walk over and lay out. Doing so she finds that she is on what has to be the biggest couch she has ever seen almost as big as her van is. She can't help it if sleep catches up with her and she quietly drifts off.

 

Minutes, maybe Hours later she is roughly awakened by someone shaking her awake violently. Before she can even realise what she is doing she reacts punching the person in the face. There is a cry of pain as they stagger back and Skye immediately jumps to her feet. 

"What the fuck?" They ask pulling ear hand away from their face covered in blood.

It is then that Skye's brain finally catches up and she looks at who she's hit, she hit Tony Stark, she punched Iron Man in the face. And if she is correct, she broke his nose, part of her doesn't know weather to be proud or terrified.

Her mind runs a million miles a minute trying to come up with what to say and Instead what comes out is "Hi, I'm Skye, and I think I'm your daughter"


	4. Chapter 4

Tony freezes and blinks once… Twice… Three times, his hand doesn't move from his slowly swelling face as blood drips. When suddenly he says "look, don’t get me, wrong kid, I don’t remember most of the 90`s, but I think I'd remember having a kid, so how about you tell me who you really are."

"I am serious," Skye insists. 

"As am I, so just tell me who you are already," Tony says becoming visibly annoyed. 

Skye sighs and says "J.A.R.V.I.S. access file #120555987145 password: pirate."

"cloud access granted, ghost drive accessed" comes J.A.R.V.I.S's confirmation. 

Tony looks momentarily stunned before asking "J.A.R.V.I.S., what just happened?"

"I'm sorry sir, but Ms Skye appears to have overwritten my protocols," J.A.R.V.I.S. replies.

"what did you do?" he asks Skye looking both suspicious and impressed.

Skye rolls her eyes saying"Jarvis display file 457221 please."

"Yes Ms. Skye," J.A.R.V.I.S says 

"Take a look if you don’t believe me," she says indicating the now floating holographic document that hangs beside them.

Tony looks at her warily before stepping over and beginning to read through the document. As he gets further, he becomes. Visibility more and more infuriated until he reaches the end and reads the name and signature at the bottom.

"J.A.R.V.I.S, is it real?" He grinds out through clenched teeth.

"All indications are that it is real sir, the document links back to Director Fury" J.A.R.V.I.S replies.

Tony turns to look at Skye, and for the first time since waking up, she is terrified of what he is going to say. He looks at her a few moments before saying "I am sorry, perhaps we can talk more when I get back, I have a pirate I need to go kill" before taking off in a sprint for the nearest balcony and jumping as a suit forms around him.

Skye sighs before sitting down "J.A.R.V.I.S?" She asks.

"Yes Ms. Skye?" He enquires.

"Can you please make sure he actually doesn't kill Fury, I've just met my father, and I'd rather not spend the next 20 years talking to him through the bars of a S.H.I.E.L.D jail cell" she requests rubbing her temples.

"As you wish."

"Thank you J.A.R.V.I.S," she says. 

"Any time ma'am."


	5. POV Switch, Tony confronts Fury

**Notes for the Chapter:**

> Errors as always are my own, my internet sucks and this was written in a break from exam study on an ipad

Ok, so he was pissed, actually no, pissed was an understatement he was furious, irate, murderous.

How dare he? How dare Fury hide his daughter away from him like that? 

The only living family he had and Fury dumped her in an orphanage. He couldn't even be fucked finding her a decent home. And yes Skye hadn't said as much in so many words but he knows the look in her eyes, he's seen it often enough on the faces of those they are called to save and it was a look he never wanted to see on his daughter's face. 

Honestly knowing he had been that much of a slouch, that shit of a person, that he didn't even know he had a daughter let alone allowing her to grow up in a orphanage. That would haunt him to the day he dies. 

And if he has his way, he will haunt Fury until the day he dies which again hopefully won't be too far away, ETA 6 minutes according to his arrival time.

As soon as he touches down on the helicarrier people are trying to flag him away from Fury. Even Maria Hill tries to redirect him saying he's in a meeting with the World Security Council. But honestly, by his point, he's barely keeping it together. No one can stop him as he barges into the teleconference room which quickly shuts down whatever Fury had been doing.

Fury barely manages to get out "Stark, what the hell…" before his fist collides with the man's face.

Behind him Maria pulls her sidearm even as she knows it won't help but Tony doesn't care he advances again punching Fury in the gut dropping him to the ground.

"You son of a bitch, you stole my daughter from me," Tony says as his fist makes contact

He looks at the man now doubled over and can barely restrain himself from finishing him but instead he says "If you ever come near me, the Avengers, or Skye again I WILL END YOU" before spinning on his heel and walking back out the way he came.

 

As Tony flies back toward the tower a team of medics finally arrive but Fury waves them off instead saying to Maria "that was unexpected"

Maria scoffs "she was his only living family and you stole her from him what did you think would happen when he found out?"

"I honestly never expected he would find out" he says clutching what feels like bruised ribs

Maria laughs humourlessly "Yeah, and look how well that turned out, I'd be careful if I were you Nick, or one day someone might just finish the job"

"I'll take that under advisement" Fury groans before making his way out of the room.


	6. Maybe, Just Maybe She is Finally Home

Skye is sitting in the lounge as she waits for Tony to return and honestly, she's utterly bored. Something about her mind means that she can very easily get bored, sure she can entertain herself given some sort of medium, i.e. by creating a method for improving the ark reactor, theoretically building elements in her head, or running through system code. But when she is sitting in a room with nothing to do she gets easily bored. That is why by the time Tony returns from his talk with Fury she has built a heat ray from the toaster that sat on the bench and a few other things she found lying around.

As soon as she sees him enter she raises an eyebrow at him in a silent question. 

Tony sighs before stepping out of the suit as he confirms "The Pirate`s alive."

Skye nods her approval before turning back to the heat ray she was building, tweaking a bit of the coil alignment.

Tony for his part seems curious as he steps over and looks at what she`s working on when he asks "what is that?"

"a heat-ray," Skye says casually

Tony looks shocked then proud, but then he seems to notice something "is that my toaster?" he groans

Skye shrugs a little before walking over to the loaf of bread that sits on the side. Without hesitation she points it at the loaf and toasts the entire thing in one go "works a bit better now" she says smirking

Tony looks between her and the casual destruction of the laws of physics before smiling brightly "kid, you and I are going to get along splendidly.” 

“Come with me I want to show you something," he says before walking toward the elevator.

Skye stops off to grab her laptop bag before quickly following and as soon as she steps into the elevator they are off. Jarvis takes them up a couple of floors before letting them out into what appears to be a workshop.

Tony smiles brightly as he says, "while I understand the urge next time just come up here if you want to build anything." 

 

He indicates the floor wide room the entirety of which is filled with bench space and assorted bits and pieces. "We have every material you could imagine, and this way Pepper doesn’t get pissed off because her toaster is missing, cool?"

Skye can only nod as she looks around, but Tony interrupts before she can really explore "Skye?"

Skye turns to face him "yes?"

"we need to talk first," he says

Skye`s blood freezes and immediately every rejection she has ever experienced runs through her mind. Luckily though Tony seems to realise this remarkably fast for someone who is supposed to not be a people person "it's nothing bad I assure you, I just want to discuss some things" he says mentally kicking himself for screwing up already

"Ok," Skye says in a small voice

Tony does his best to be comforting as he waves her toward one of the nearby walls where a long couch rests. As soon as they are seated, he says "I just, I wanted you to know. I had no idea, about any of this, if I had known I never would have allowed Fury to do this"

Skye raises an eyebrow at him waiting for him to continue as her walls slowly creep higher.

He continues his voice creaking "I grew up with parents who were never around, and I swore I would never allow my kids to grow up that way. I may have been an ass, still am" he gives a small self-depreciating smile before continuing more solemnly "but if there's one thing that I want you to know, it's you were always wanted." Skyes mind grinds to a halt "I don’t know how Fury managed to do what he did, but I will do everything in my power to make up for it ok?" he asks

 

But Skye`s mind has already frozen, that one sentence repeating in her mind over and over again "you were wanted" one sentence that she has dreamed of hearing for years, one sentence that manages to slam down all her walls in one blow. Part of her mind is screaming at her this isn't to be trusted, that this will be taken from her too, that he like everyone else won't mean it once he gets to know her. But another part of her screams at her to trust him, he's her father, the person she has been searching for years to find. He is like her in so many ways, and it is this that finally convinces her to trust him, to give him a chance.

"Skye?" he asks with a shaking voice, and it is clear he fears her reaction. But it causes something in her to break, that last piece of composure to shatter and in a flash, she is hugging him tightly as his arms come to rest around her as he says "Shhh… Shhh… It`s ok, it will all be ok."


	7. Meet Pepper

As it turns out when they weren't overly emotional as Skye called it Tony and Skye acted more or less like a self-reinforcing bond, propelling the other deeper into SCIENCE!!! 

As soon as they had recovered from the emotional toll of their earlier conversation they had started going through the lab with a vengeance. Skye immediately bringing Watchtower in to assist alongside J.A.R.V.I.S.

Tony was amazed at the complexity and scope of the AI she had built in so little time. After a moments consideration, he even decided to do a side by side comparison between Skye's AI and J.A.R.V.I.S. and what he saw amazed him.

Watchtower was like J.A.R.V.I.S. on steroids; it was like looking at his MK1 and the MK42 side by side. Having seen this, there was no doubt in his mind that Skye was utterly brilliant, more so perhaps than himself and so he set about giving her little challenges.

 

For hours they work side by side as Tony watches amazed at the way Skye instinctively grasps high-level coding and quantum mechanical theorem. It is nearly 19 hours later that they actually stop at almost 2:30 the next day and even then it's only because Pepper having not heard from Tony came to drag him out of the lab.

 

As soon as she enters Tony practically bounces over like an overexcited child saying "Pepper, Pepper, quick come see" and tugging her back over to where Skye is working

Pepper quickly acquiesces hoping that whatever Tony has built this time it isn't another weapon. She starts to say "Tony, I'm glad you're excited, but do you really need another… Weapon" she freezes at the sight of Skye who momentarily looks up before becoming engrossed back in what she is working on.

'Oh god, there's two of them' she thinks before turning to Tony and quirking an eyebrow in question

Tony beams at her and says "Pepper, meet Skye, my daughter."

Pepper freezes and turns to look at him wide-eyed before saying a single word "explain."

And so Tony does, he tells her as much as he knows or has guessed about how Fury had hidden Skye and already Pepper is planning a very unpleasant meeting for Fury in the near future. But for the moment she puts that aside instead turning to Skye and saying "It's a pleasure to meet you, Skye, I'm Virginia Pepper Potts, but please call me Pepper."

Skye turns to really look her over, and Pepper sees a look on her face she's seen all too often over the years as Skye seems to size her up before quickly glancing to Tony whom nearly imperceptibly nods and saying "Skye, just Skye, nice to meet you too."

Tony nods pleased by the interaction before moving back toward the bench saying "you'll never believe it Pep, Skye built a self-regenerating miniaturised arc reactor, isn't she amazing."

Pepper looks at the young woman who seems to be blushing at the praise before saying "indeed, but unfortunately, that will have to wait, you have been down here for near on 20 hours, you need to sleep, both of you."

Skye looks bashful before putting down her tools and beginning to get up but Tony groans "Pepper, we were just…"

Pepper cuts him off "uh uh Tony Stark, you're a father now and like it or not that means being responsible. So the both of you, go, sleep, I'll tell J.A.R.V.I.S. not to let you in here for the next 12 hours, SCIENCE! Can wait."

"Fine" Tony groans then he realises something "hey Skye I just realised, we haven't set you up a room yet."

Pepper turns to look at him before releasing a long-suffering sigh of disbelief "Tony you didn't set up a room for her yet? Fine, you two can be here for another hour while I arrange things but one minute more, and I send Cap and the others to drag you out clear?"

"Yes, Pepper" they chorus before turning back to the project at hand as Pepper shakes her head and walks toward the elevator "J.A.R.V.I.S, contact the movers, we need some things brought up."

"Yes Ms Potts" comes the ever faithful response


End file.
